Vaccines
You might have heard that the USA is having an egg shortage. You might know that 80% of flu vaccines are made with eggs. You might get concerned that egg-based vaccine production would be impacted. Fear not! This article (2025-02-19) reports that chickens who lay vaccine eggs are raised in a “controlled environment”, so aren’t getting sick. (This article (paywalled, 2019-01-25) talks a little bit about what “controlled environment” means.) This paper, in fact, from WHO (2025-02-20) reports that vaccine production capacity has stayed very stable since 2019.
Speaking of egg-based vaccines, this article (2017-11-06) discusses how growing viruses in eggs is not ideal: the viruses sometimes adapt to the egg environment in ways that are not helpful to humans, which is part of why flu vaccines don’t have high effectiveness. A number of companies are moving away from egg-based vaccines, but the vast majority of the seasonal flu shots are still made in eggs: it’s cheap and a very mature technology.
Recommended Reading
This article (2025-02-21) is not exactly about the pandemic, but it is about virology research and uncatalogued viruses — which could turn into a pandemic. The article discusses Human Virome Program, which aims to catalogue all the viruses in the humans’ bodies. (Yeah, ambitious.) The article also has some interesting asides, like that certain viruses actually seem to give some benefit to humans, like cytomegaloviruses might help defend us against skin cancer. Who knew?!?!
COVID-19
🦇 Oh great. This paper from China (2025-02-18) reports that scientists have found another virus in bats which targets the human ACE2 receptor (i.e. has enormous spillover potential). But waits, it gets even worse: it’s not even a sarbecoronavirus like COVID-19, it’s a merbecovirus, like MERS 🐪. 😬
Now, it has not (yet) jumped to humans. It just looks like it could.
Long COVID
😢 This paper from USA (2025-02-13) reports that only 2% of the long haulers in their study recovered — even after three years.
AGAIN This preprint from Australia (2025-02-12) reports finding 32 genes — 19 of which had been found before, 13 of which were new — that affect one’s risk of getting Long COVID. Some increase the risk, some decrease the risk.
AGAIN This paper from Spain (2025-02-11) reports that vaccination drops your risk of Long COVID in about half. This was even after adjusting for a long list of things: sex, age, university education, body mass index, physical activity, race, tobacco use, alcohol intake, adherence to Mediterranean diet, previous illness, flu vaccination, health care worker, high-risk COVID worker and sleep hours and sedentarism. It was done by comparing surveys from
- people who got COVID-19 infections without Long COVID
to surveys from
- people who did get Long COVID.
This preprint using data from USA and UK(2025-02-06) reports that genes found to be related to Long COVID by looking at an overwhelmingly white cohort were also found in a more diverse cohort. (The authors looked for 73 genes related to Long COVID that a previous study found; I don’t know if the authors of the Australia preprint I referenced in the previous snippet knew about these 73, and I didn’t take the time to cross-reference them all.)
🤔❓ This paper from USA (2025-02-19) found that more than a fifth of US adults had high confidence in their Long COVID knowledge despite being pretty clueless. I can’t decide if that’s funny or sad.
🩸 This paper from USA (2025-02-17) reports that Long COVID patients have a lower density of capillaries in the deep areas of their retinas than controls. They don’t know about deep capillaries in other parts of the body — you can’t just look at them like you can with eyeballs — but if deep capillaries are missing in other parts of the body, that means there are a bunch of cells which are getting starved for oxygen. 😬
🧠 This paper from Switzerland (2025-01-21) reports finding T2-hyperintense lesions on MRI scans of 72% of Long COVID patients’ brains. (T2-hyperintense lesions is a fancy way of saying “white spots on the image”; there are a number of different things that can cause them.) They found that the number of lesions didn’t correlate with fatigue or headache. I also don’t know how many lesions healthy controls have. This paper (2019-12-09) says that “white matter hyperintensities were common at age 45”.
🩸‼️ This paper from Belgium (2025-01-25) reports that Long COVID patients found that Long COVID patients had elevated levels of thrombin, an enzyme which promotes clotting.
❤️🩹 This paper from UK (2025-02-14) reports that patients with a history of COVID-19 had worse cardiac scores on some (but not all) measures of cardiovascular fitness than people without a COVID-19 history. The COVID-19 cohort had lower O2 consumption at anaerobic threshold, peak cardiac index, and peak stroke volume index.
🦷 This paper from USA (2025-02-19) reports that COVID-19 history significantly correlates with severe oral health complications in predominantly Black communities, while vaccination reduced but did not eliminate these issues. People who had had COVID-19 infections had a bit over twice the risk of developing gum disease as people who hadn’t had COVID-19 infections. Gum disease correlated with dry mouth, loss of smell, and taste disturbances. They also found signs that the virus wasn’t getting cleared: three to six months after the COVID-19 infection, about 70% of the COVID-19 cohort had spike proteins in their saliva, compared to only 6% of the non-COVID cohort. They also found a ton of oral viruses in the COVID-19 cohort, including Epstein-Barr Virus (in 70.5% of the patients), Herpes Simplex Virus (8.1%), and Human Papillomavirus (17.5%).
I have seen other papers which said that people who got sicker with COVID-19 had worse oral health, so I have to wonder about the direction of cause and effect in this study.
They also implied that this study was going to be about differences between different ethnic groups, but I didn’t see anything in the paper about that.
Transmission
This article from USA (2025-02-11) says that flu deaths passed COVID-19 deaths in the USA for the first time since the pandemic started. (Yes, it’s the USA and not Canada, but they are our neighbours.)
People sometimes say that COVID-19 “is just like the flu”, by which they really mean “just like a cold”, which is not true. COVID-19 has a master key to get easily into almost all human cells, AND influenza is nasty even with only the keys to get easily into respiratory cells!
Vaccines
💉 This preprint from USA (2025-02-19) examines the (very small number of) people who get Long COVID-like symptoms from vaccination. (This article (2025-02-20) discusses the preprint in some detail but it is paywalled.) People with post-vaccination syndrome (PVS) have different immune cell profiles than healthy controls; a lot of them showed signs of Epstein-Barr Virus re-activation, and a lot had COVID-19 spike proteins circulating in their body way past what is normal and reasonable.
Mitigation Measures
This press release (2025-02-08) describes this personal air cleaning product. Air is disinfected with a cold plasma, then run to a hard hat-looking helmet, and air is blown down, making what they call an “air curtain” that keeps out pathogens. It’s currently in beta testing, so maybe if you are interested you be a beta tester? (I sent them email volunteering to be a beta tester but have not heard back.)
Testing
🌬️ This preprint from Japan (2025-02-19) reports that researchers were able to detect COVID-19 in the air by using techniques similar to those used in detecting pathogens in wastewater. The amount seen correlated with the number of COVID-positive people in the room, so this could perhaps also be used to estimate how many people have COVID-19 nearby.
Culture/Politics
This article (paywalled, 2025-02-18) notes the shift to the right (especially in young men) in multiple countries, and suggests several ways which the pandemic might have encouraged that shift.
- economic upheaval;
- less trust in public institutions;
- more screen time and less face-to-face time, which leads to higher polarization of boys and girls.
I’m now wondering how much of WW2 was a reaction to the 1918 influenza pandemic!
Recommended Reading
This blog post (2025-02-20) has an interesting thesis: it says that the swing towards fascism is <waves hands> because The Rich got freaked out by all the welfare state stuff that was implemented during the early pandemic which actually worked. Direct cash payments, eviction bans, debt collection bans, homeless people given shelter, free food, remote work normalized, etc. It goes on to say that this led to reductions in poverty, reductions in homelessness, plummeting suicide rates, a true sense of collectivism, and massive protests against racism (because, he says, people had time to protest).
H5N1
Transmission
🪿🌬️ ➡️🐔😬😬 This preprint from Czech Republic (2025-02-12) claims to have demonstrated transmission of H5N1 through the air between an infected duck farm (the index farm) and two biosecure poultry farms around 8 kilometers away. They say that the genetic signatures were identical or very similar at the three locations (and in some ill backyard poultry that were probably infected at about the same time as the index farm), and that weather data showed that the wind movements were consistent with airborne spread. The different farms were in different market segments, and interviews with personnel at the index farm didn’t find any people who had worked at the others (including e.g. feed suppliers). There was a big lake near the index farm and backyard poultry where lots of wild birds congregated, but there weren’t any lakes near the other two farms.
I sure hope that transmission through the air for 8km is not an easy way for H5N1 to spread! 😬
🐦⬛➡️🐄This article (2025-02-17) reports that an infection in a dairy herd in Arizona was from the bird version of bird flu – clade D1.1, and is genetically far enough from the Nevada D1.1 outbreak that it looks like it is not related to the Nevada outbreak. This makes the third known spillover from birds to cows in the USA.
Everyone had been hoping that there had been just one spillover event, that they were rare, and the Nevada D1.1 infection plus this Arizona D1.1 infection kinda puts the kibosh on that hope. In particular, this means that Canadian herds are at risk even if we never ever import another cow from the USA.
(NB: This was found via routine bulk testing of milk, yay routine bulk testing!)
This article (2025-02-18) reports that there have now been 972 dairy herds in the USA found to be infected, with 747 in California.
🐦⬛➡️🐔 This report preview (2025-02-13) says that some backyard poultry in Newfoundland and Labrador was discovered to be infected with H5N5. The “H5” part was the same as the (now, alas, bog-)standard H5N1, but the “N5” part is something presumably imported from Europe. They’ve seen a fair amount of H5N5 in Europe, and a lot of birds from Europe visit NL.
🧍➡️🐈☠️ This report from the US CDC (2025-02-20) says that three indoor housecats in Michigan in two households were found to have H5N1 in May. The three cats both lived households with a dairy worker in a county which had known H5N1 infections. Both of the dairy workers declined H5N1 testing, but it seems pretty clear to me that the humans transmitted H5N1 to their cats. 😬 One of the cats was known to roll in the work clothes of the dairy worker, which had milk splashes on them.
Some good news: One cat in one of the households did not get sick. In one of the households, three other members of the household agreed to H5N1 testing, and they were all negative — although they tested late and might have already recovered.
Vaccines
💉 This press release from the Government of Canada (2025-02-19) reports that the government has purchased 500,000 doses of GSK’s human vaccine against avian influenza (GSK’s ArepanrixTM H5N1 A/American wigeon clade 2.3.4.4b). They are going to send 60% to the provinces and hold 40% in reserve with the federal government. While they aren’t planning on doing mass vaccinations, this press release (2025-02-19) from the National Advisory Committee on Immunization developed a decision matrix to figure out who to give doses to when in a “non-pandemic context”. Basically, it’s people who have contact with potentially infected animals, in the context of various severities of outbreaks.
500,000 obviously isn’t enough for everybody, but it certainly is better than zero and ought to be enough to protect people at most risk. I am glad that they bought the doses and developed the decision matrix.
💉🐔 This article (2025-02-18) reports that the US Department of Agriculture has given conditional approval to a H5N1 vaccine for poultry. Interesting side note: the article mentions that the vaccine got conditional approval once before, in 2023 to help protect the endangered California Condor. This doesn’t mean that anybody can buy and use the vax yet, however — it’s just one of the normal steps towards approval.
Poultry farmers are apparently divided over whether they like the idea of vaccination or not. It could save their birds but as this article (2024-05-14) describes, there are many countries which will not accept meat/eggs/breeders from countries that allow vaccinating poultry because of the fear of importing infected birds. (The article about trade says that bird flu vaccination doesn’t stop the infection, it just keeps the chicken from becoming unwell.)
🐀 This article (2025-02-19) reports that the USDA has found bird flu in rats. Given how closely rats live to humans, I find this unnerving. 😬
Treatments
💊 This paper from Canada (2025-02-20) reports that Paxlovid doesn’t help vaccinated people all that much. They compared electronic records of people between 65 and 74, and looked at how the under-70 compared to the over-70, since 70 was the cutoff for Paxlovid eligibility. They found that there wasn’t a significant difference between the just-over-70s and the just-under-70s in hospitalization or all-cause mortality. At best, the utility of Paxlovid was four times lower than in the original Paxlovid trial (which looked at middle-aged unvaccinated adults).
Variants
This paper from Canada (2025-02-18) reports that a variant found in a very small number of poultry in BC has a mutation (H275Y) which is known to give resistance to Tamiflu. Great.
Economics: Birds vs. Cows
This article (2025-02-20) explains (part of) why H5N1 in cattle is such a fustercluck in the USA.
- Chickens go to “processing plants” in batches, all together, about seven weeks after they come in, so killing off all the chickens means you only lose seven weeks of work. Cows live a long time and come and go as individuals, not as a batch with the entire herd.
- Cows are a lot more expensive than chickens.
- Essentially all the chickens that get H5N1 die anyway, so culling them just saves some time. Only about 1% to 2% of cows which get H5N1 die.
- For a long time, there have been rules on the books that compensate farmers for chickens that authorities cull. (I’m not sure if it’s Big Chicken or the farmers; the article says “farmers”, but Big Chicken owns the birds, so I’m not sure.) There is no mechanism to compensate farmers for culled cattle.
- The article only mentions this very slightly in passing, but the way the US chicken industry is set up, the farmers don’t own the chickens: they only provide chicken-raising services to the Big Chicken companies which own the birds. Farmers own their cattle.
The article mentions that while H5N1 is much more deadly in chickens than cows, H5N1 in cattle is — in theory — more dangerous to humans, given that cattle and humans are both mammals. Mutations in H5N1 to make it more suited to cows will also make it more suited to people. (Note that this doesn’t actually square with the most severe cases in humans being from the bird clade of H5N1 instead of from the cattle clade.)
This article mentions in passing that roughly 10 percent of all laying chickens have died in the last three months.
Mystery Illness
🦇 Remember the mystery illness in DR Congo? It’s not gone, and this article (2025-02-21) reports that recent tests have said it isn’t Marburg or Ebola. And, I’m sure you’ll be not pleased to hear that some kids who died had recently eaten bats. 😬